tbuckley/cabot-search huggingface dataset:
Autoencoders for sample size estimation for fully connected neural network classifiers
Authors: Faris F. Gulamali, Ashwin S. Sawant, Patricia Kovatch, Benjamin Glicksberg, Alexander Charney, Girish N. Nadkarni, Eric Oermann
Journal: npj Digital Medicine (2022)

Abstract Sample size estimation is a crucial step in experimental design but is understudied in the context of deep learning. Currently, estimating the quantity of labeled data needed to train a classifier to a desired performance, is largely based on prior experience with similar models and problems or on untested heuristics. In many supervised machine learning applications, data labeling can be expensive and time-consuming and would benefit from a more rigorous means of estimating labeling requirements. Here, we study the problem of estimating the minimum sample size of labeled training data necessary for training computer vision models as an exemplar for other deep learning problems. We consider the problem of identifying the minimal number of labeled data points to achieve a generalizable representation of the data, a minimum converging sample (MCS). We use autoencoder loss to estimate the MCS for fully connected neural network classifiers. At sample sizes smaller than the MCS estimate, fully connected networks fail to distinguish classes, and at sample sizes above the MCS estimate, generalizability strongly correlates with the loss function of the autoencoder. We provide an easily accessible, code-free, and dataset-agnostic tool to estimate sample sizes for fully connected networks. Taken together, our findings suggest that MCS and convergence estimation are promising methods to guide sample size estimates for data collection and labeling prior to training deep learning models in computer vision.
Changes in signalling from faecal neuroactive metabolites following dietary modulation of IBS pain
Authors: Caroline J Tuck, Amal Abu Omar, Giada De Palma, Samira Osman, Nestor N Jiménez-Vargas, Yang Yu, Sean MP Bennet, Cintya Lopez-Lopez, Josue O Jaramillo-Polanco, Corey C Baker, Aidan SW Bennett, Mabel Guzman-Rodriguez, Quentin Tsang, Taylor Alward, Sebastien Rolland, Celine Morissette, Elena F Verdu, Premysl Bercik, Stephen J Vanner, Alan E Lomax, David E Reed
Journal: Gut (2022)

Objective Dietary therapies for irritable bowel syndrome (IBS) have received increasing interest but predicting which patients will benefit remains a challenge due to a lack of mechanistic insight. We recently found evidence of a role for the microbiota in dietary modulation of pain signalling in a humanised mouse model of IBS. This randomised cross-over study aimed to test the hypothesis that pain relief following reduced consumption of fermentable carbohydrates is the result of changes in luminal neuroactive metabolites. Design IBS (Rome IV) participants underwent four trial periods: two non-intervention periods, followed by a diet low (LFD) and high in fermentable carbohydrates for 3 weeks each. At the end of each period, participants completed questionnaires and provided stool. The effects of faecal supernatants (FS) collected before (IBS FS) and after a LFD (LFD FS) on nociceptive afferent neurons were assessed in mice using patch-clamp and ex vivo colonic afferent nerve recording techniques. Results Total IBS symptom severity score and abdominal pain were reduced by the LFD (N=25; p&lt;0.01). Excitability of neurons was increased in response to IBS FS, but this effect was reduced (p&lt;0.01) with LFD FS from pain-responders. IBS FS from pain-responders increased mechanosensitivity of nociceptive afferent nerve axons (p&lt;0.001), an effect lost following LFD FS administration (p=NS) or when IBS FS was administered in the presence of antagonists of histamine receptors or protease inhibitors. Conclusions In a subset of IBS patients with improvement in abdominal pain following a LFD, there is a decrease in pronociceptive signalling from FS, suggesting that changes in luminal mediators may contribute to symptom response.
Antibody feedback contributes to facilitating the development of Omicron-reactive memory B cells in SARS-CoV-2 mRNA vaccinees
Authors: Takeshi Inoue, Ryo Shinnakasu, Chie Kawai, Hiromi Yamamoto, Shuhei Sakakibara, Chikako Ono, Yumi Itoh, Tommy Terooatea, Kazuo Yamashita, Toru Okamoto, Noritaka Hashii, Akiko Ishii-Watabe, Noah S. Butler, Yoshiharu Matsuura, Hisatake Matsumoto, Shinya Otsuka, Kei Hiraoka, Takanori Teshima, Masaaki Murakami, Tomohiro Kurosaki
Journal: The Journal of Experimental Medicine (2022)

In contrast to a second dose of the SARS-CoV-2 mRNA vaccine, a third dose elicits potent neutralizing activity against the Omicron variant. To address the underlying mechanism for this differential antibody response, we examined spike receptor-binding domain (RBD)–specific memory B cells in vaccinated individuals. Frequency of Omicron-reactive memory B cells increased ∼9 mo after the second vaccine dose. These memory B cells show an altered distribution of epitopes from pre-second memory B cells, presumably due to an antibody feedback mechanism. This hypothesis was tested using mouse models, showing that an addition or a depletion of RBD-induced serum antibodies results in a concomitant increase or decrease, respectively, of Omicron-reactive germinal center (GC) and memory B cells. Our data suggest that pre-generated antibodies modulate the selection of GC and subsequent memory B cells after the second vaccine dose, accumulating more Omicron-reactive memory B cells over time, which contributes to the generation of Omicron-neutralizing antibodies elicited by the third vaccine dose.
Mutations in SARS-CoV-2 spike protein impair epitope-specific CD4+ T cell recognition
Authors: Emily X. C. Tye, Elizabeth Jinks, Tracey A. Haigh, Baksho Kaul, Prashant Patel, Helen M. Parry, Maddy L. Newby, Max Crispin, Nayandeep Kaur, Paul Moss, Samantha J. Drennan, Graham S. Taylor, Heather M. Long
Journal: Nature Immunology (2022)
Interactions Between Genetic Risk and Diet Influencing Risk of Incident Female Gout: Discovery and Replication Analysis of Four Prospective Cohorts
Authors: Kehuan Lin, Natalie McCormick, Chio Yokose, Amit D. Joshi, Na Lu, Gary C. Curhan, Tony R. Merriman, Kenneth G. Saag, Paul M. Ridker, Julie E. Buring, Daniel I. Chasman, Frank B. Hu, Hyon K. Choi
Journal: Arthritis & Rheumatology (2022)

Objective To examine whether the cross‐sectional gene–diet interaction for prevalent hyperuricemia among women translates prospectively to risk of incident female gout. Methods We analyzed the interaction between genetic predisposition and adherence to a healthy dietary pattern (i.e., Dietary Approaches to Stop Hypertension [DASH] score) on risk of incident female gout in 18,244 women from Nurses’ Health Study (NHS; discovery) and 136,786 women from 3 additional prospective female cohorts from the US and UK (replication). Genetic risk score (GRS) was calculated from 114 urate‐associated loci. Results In the NHS and replication cohorts, association between diet and gout risk was larger and stronger among women with higher genetic risk. In all cohorts combined, compared to women with an unhealthy DASH score (less than the mean score), multivariable relative risk (RR) for incident gout among women with a healthy DASH score (greater than/equal to the mean score) was 0.67 (95% confidence interval [95% CI] 0.60–0.76) among higher GRS (greater than/equal to the mean score) and 0.91 (0.78–1.05) among lower GRS ( P for multiplicative interaction = 0.001); multivariable RR for higher versus lower GRS was 2.03 (95% CI 1.80–2.29) and 1.50 (95% CI 1.31–1.71) among unhealthy and healthy DASH score groups, respectively. Additive interaction was also significant, in both the discovery and replication cohorts ( P &lt; 0.001), with 51% of the excess risk attributable to the additive gene–diet interaction in all cohorts combined. Conclusion The deleterious effect of genetic predisposition on risk of incident female gout was more pronounced among women with unhealthy diets, with nearly half the excess risk attributable to this gene–diet interaction. These data elucidate the important synergy of genetics and diet for female gout development. image
When less is more: The way forward for mental health interventions during the perinatal period
Authors: Mark Tomlinson, Mary Jane Rotheram-Borus
Journal: PLoS Medicine (2022)

Globally, almost 40 million people are living with HIV, with almost half of these being women of childbearing age [1].In addition, depression is a leading cause of disability globally, but despite these high levels, data for low-and middle-income countries (LMICs) is limited-particularly in the context of HIV [2].Given this context, the work of Kaaya and colleagues [3] describing a peer-facilitated psychological group intervention (Healthy Option) for perinatal women living with HIV and receiving ART is welcome.The study was a cluster randomised controlled trial conducted in urban districts of Dar es Salaam.Utilising community-based health workers trained in problem solving and cognitive behaviour therapy for women screened for depression risk.While the Healthy Options intervention showed no benefit for a reduction in depressive symptoms at 9 months postpartum (primary outcome), there was a benefit for depressive symptoms at 6 weeks postpartum [3].This is an important study adding to the growing evidence base of interventions for improving mental health in the perinatal period in LMICs.Having said this, there are a number of key areas that we believe bear discussion in thinking about the way forward for the design and evaluation of perinatal mental health interventions such as this one.In this commentary, we focus on 4 aspects: (1) screening for as opposed to diagnosing depression; (2) continued creation of new evidence-based interventions (EBI) versus building on existing evidence of common elements/principles, approaches; (3) applying EBI universally versus stepped care approaches; and (4) integrated versus siloed approaches.
Traction by dental floss loop for adequate submucosal dissection depth in a rectal neuroendocrine tumor
Authors: Jianning Liu, Nian Fang
Journal: Endoscopy (2022)

The European Society of Gastrointestinal Endoscopy (ESGE) recommends modified EMR (mEMR) as the first option for removing rectal neuroendocrine tumors (rNETs), since mEMR was shown to be superior to endoscopic submucosal dissection (ESD) for histological complete resection [1] [2]. In rNETs, deep mucosa and submucosa are involved, and therefore adequate submucosal dissection depth is essential to achieve complete resection. A loop of dental floss has been previously reported to enable proper access to the submucosal layer and could potentially be useful for achieving deeper resection in ESD [3]. We present a case of a small rNET successfully treated by loop-traction-assisted ESD ([Video 1]).
Endoscopic management of bleeding after endoscopic ultrasound-guided drainage of a pancreatic pseudocyst
Authors: Yaoting Li, Lichao Zhang, Tingting Yu, Hongfei He, Senlin Hou
Journal: Endoscopy (2022)

A 64-year-old man was admitted to our hospital with abdominal bloating. Computed tomography revealed a pancreatic pseudocyst located caudal to the body of the pancreas ([Fig. 1]). Endoscopic ultrasound (EUS)-guided pancreatic pseudocyst drainage was performed. We used a 19-gauge fine-needle aspiration needle to target the gastric wall. A 0.035-inch guidewire was advanced through the needle and the tract was dilated to 12 mm. A plastic double-pigtail stent and a nasal cystic drainage tube (7 Fr) were then placed into the passageway between the stomach and the cyst.
Endoscopic strictureplasty for severe colonic anastomotic stricture
Authors: Shunya Takayanagi, Ken Ohata, Yoshiaki Kimoto, Rindo Ishii, Ryoju Negishi, Yohei Minato, Kentaro Nakajima
Journal: Endoscopy (2022)

Benign anastomotic stricture after colonic resection usually requires surgical or endoscopic dilation. The radial incision and cutting (RIC) method was recently developed to treat resistant strictures and the recurrence rate is 28.5–44.2 % [1] [2]. In this report, we developed endoscopic strictureplasty (ESP) for refractory anastomotic stricture after colorectal surgery not resolved by two RICs.
From darkness to brightness: the cholangioscopy-guided selective biliary cannulation with the help of transparent cap during ERCP
Authors: Wei-hui Liu, Xin-yu Huang, Ren-yi Zhang, Rui Huang, Si-yu Qin, Xiao-gang Liu
Journal: Endoscopy (2022)

Endoscopic retrograde cholangiopancreatography (ERCP) is recommended as the primary treatment for choledocholithiasis [1]. Selective biliary cannulation is the most challenging step for ERCP since only an indirect image under X-ray can be obtained, and this process largely determines the occurrence of postoperative pancreatitis [2] [3]. Simultaneous repeated X-ray irradiation adversely affects the health of operators and patients [4]. To solve these problems, we have developed a novel biliary cannulating technique under direct vision of the cholangioscope, whose tip is covered by a conical transparent cap ([Video 1]).
Underwater and traction-assisted endoscopic submucosal dissection in the gastric fundus using a multibending endoscope
Authors: Koichi Hamada, Yoshinori Horikawa, Yoshiki Shiwa, Kae Techigawara, Masafumi Ishikawa, Noriyuki Nishino, Michitaka Honda
Journal: Endoscopy (2022)

The gastric fundus is the most challenging site for endoscopic submucosal dissection (ESD) because accessing the fundus with the tip of the endoscope is difficult. Furthermore, the wall of the fundus is thin and the knife-edge is pointed towards the muscle layer. A combination of the previously reported effective methods, namely, a multibending endoscope [1], multiloop traction [2], and underwater technique [3] may offer safe treatment in the fundus. Herein, we report a successful ESD performed by a trainee using these three methods.
Emergency call: “Doctor I swallowed a stick”
Authors: Cándida M. Leiva Pineda, Katherine E. Maldonado Cardona, María J. Solorzano Alfaro, Luis F. Quevedo Alvarado, Abel A. Sánchez Orozco, Evelyn R. Mena Pineda, Eliú C. Hernández Cordón
Journal: Endoscopy (2022)

Foreign bodies represent one of the most frequent emergencies in the practice of gastroenterology. About 80 % of cases resolve or the foreign body is passed spontaneously. Approximately 10 %–20 % of foreign bodies require endoscopic extraction and fewer than 1 % require surgical removal [1].
Thread a needle with two hands: inner countertraction using clip with rubber band facilitates difficult pancreatic cannulation during ERCP
Authors: Ren-yi Zhang, Qiang Guo, Xiao Hu, Wei-hui Liu
Journal: Endoscopy (2022)

Difficult biliary or pancreatic cannulation during endoscopic retrograde cholangiopancreatography (ERCP) is among the leading causes of failed operations [1]. Inspired by the application of traction in endoscopic treatment of early gastrointestinal tumors [2], we have developed clip-and-rubber-band traction to accomplish difficult pancreatic cannulation during ERCP ([Video 1]).
A novel endoscopy training system by video-based asynchronous communication
Authors: Takahiro Inoue, Takahiro Utsumi, Nobukazu Agatsuma, Yoshitaka Nishikawa, Mano Soshi, Yasushi Sano, Hiroshi Seno
Journal: Endoscopy (2022)

Although instruction by experienced endoscopists is preferable for improving trainees' endoscopic skills [1] [2] [3] [4], this is not always achievable in clinical practice because of manpower shortages or other circumstances. Recently, synchronous training (e. g. hands-on seminars) has become popular among endoscopy trainees. However, the opportunities to attend these events are limited and effective instruction is difficult to achieve in a short time. Tsucom (BonBon Inc., Kyoto, Japan) is an online platform supporting video-based asynchronous communication [5]. This platform allows intra-group communication at any time and place via addition of reactions by text and audio to uploaded videos ([Fig. 1]). Herein, we demonstrate our novel training system using Tsucom for an endoscopic procedure in a porcine model ([Video 1]).
Endoscopic closure of a gastric perforation using mucosal adaptative ring to close endoscopic artificial ulcer: the MARCEAU system
Authors: Raphaëlle Grau, Mathieu Pioche, Jérôme Rivory, Pierre Lafeuille, Clara Yzet
Journal: Endoscopy (2022)

A percutaneous endoscopic gastrotomy (PEG) tube is removed after the complete resumption of oral intake. The gastrostomy site closes spontaneously in most cases after the removal of the PEG tube [1]. However, persistent gastrocutaneous fistulae can occasionally occur. They are first managed medically with a proton pump inhibitor (PPI), and in case of persistent fistulae, endoscopic management can be proposed using a hemostatic clip or over-the-scope (OTS) clip [2].
The “tapping-a-screw method” for endoscopic removal of an incarcerated pancreatic duct stone using a novel screw-shaped dilator with a 0.018-inch guidewire
Authors: Sho Kitagawa, Yasutaka Nakai, Shori Ishikawa
Journal: Endoscopy (2022)

Endoscopic intervention is an established treatment in patients with obstructive pancreatitis; however, dealing with impacted pancreatic duct stones remains challenging. Although electrohydraulic or laser lithotripsy under digital single-operator pancreatoscopy (D-SOP) is one of the feasible approaches [1], some special techniques are required in cases where D-SOP is not applicable [2] [3]. Herein, we report a method to accomplish endoscopic removal of an incarcerated pancreatic duct stone using a novel stiff screw-shaped dilator with a 0.018-inch guidewire.
A novel controllable catheter with a short flexible tip for guidewire insertion in severe malignant hilar biliary stricture
Authors: Tadahisa Inoue, Mayu Ibusuki, Rena Kitano, Yuji Kobayashi, Kiyoaki Ito, Masashi Yoneda
Journal: Endoscopy (2022)

During stenting for a malignant hilar biliary obstruction (MHBO), guidewire insertion to the intended intrahepatic bile duct is sometimes very technically challenging [1]. It is especially difficult when the bend in the bile duct is steep and involved in the stricture. A novel controllable catheter (Zeon Medical, Tokyo, Japan) with a short flexible tip is more flexible and can be bent more than conventional controllable catheters (Swing Tip cannula; Olympus Medical Systems, Tokyo, Japan) [2], which have a range of 90 degrees upwards and downwards. Furthermore, the fulcrum for the tip bend is closer to the tip (15 mm) than in the conventional catheter (30 mm) ([Fig. 1]).
Virtual scale endoscope-assisted wide-field resection of large sessile serrated lesions
Authors: Roupen Djinbachian, Daniel von Renteln
Journal: Endoscopy (2022)

Large sessile serrated lesions (SSLs) are associated with a very high risk of incomplete resection. The CARE study found almost 50 % incomplete resections among 10 to 20-mm SSLs [1]. Wide-field cold snare resection with submucosal injection (cap-assisted endoscopic mucosal resection, C-EMR) has been proposed as an effective method to prevent incomplete resection since distinguishing SSL margins during resection is difficult [2] [3] [4]. In contrast to a hot snare, a more extended resection field is recommended for a cold snare [5]. However, quantification of the resection field extent in comparison to polyp size has been challenging in the past. The novel virtual scale endoscope (VSE; SCALE EYE, Fujifilm, Tokyo, Japan) can be used as dedicated technology to measure polyp size before resection and to ensure adequate post-resection defect size. The VSE allows polyp size measurement during live colonoscopies by emitting a laser beam onto the mucosa to measure distance. This permits superimposition of a linear/circular ruler that changes in size depending on distance of the endoscope to the laser point ([Fig. 1]).
The “zipline” technique for endoscopic removal of a migrated pancreatic stent
Authors: Kohei Kurihara, Naminatsu Takahara, Tsuyoshi Hamada, Sachiko Kanai, Ryunosuke Hakuta, Yousuke Nakai, Mitsuhiro Fujishiro
Journal: Endoscopy (2022)

Prophylactic placement of a pancreatic stent can reduce post–endoscopic retrograde cholangiopancreatography (ERCP) pancreatitis (PEP), but it entails the risk of several adverse events including stent migration [1]. Endoscopic removal of a migrated stent is technically challenging because limited devices are available for use in the small and tortuous pancreatic duct [2]. Here, we present a case in which the "zipline" technique enabled successful removal of a pancreatic stent that had totally migrated into the pancreatic duct.
Capsule endoscopy successfully diagnosed Henoch-Schönlein Purpura in a patient with small intestine involvement
Authors: Shao-xiong Zeng, Han-lin Chen, Xiao-fei Yin, Chun-sheng Cheng
Journal: Endoscopy (2022)

A young woman presented with vomiting after eating shrimp and abdominal pain predominantly around the umbilicus and upper abdomen. Physical examination revealed epigastric and periumbilical tenderness without rebound tenderness. Petechiae, ecchymoses, and palpable rashes were observed in the distal part of both lower limbs ([Fig. 1]). Laboratory tests revealed an increase in CRP (38.1 mg/L), ESR (38 mm/h), and IgE (872.0 IU/ml), while the other relevant tests and physical examinations were unremarkable.
Gastric endoscopic submucosal dissection assisted by intralesional cross-traction using silicone bands
Authors: Yusuke Suzuki, Mitsuru Esaki, Taisuke Inada, Yosuke Minoda, Haruei Ogino, Eikichi Ihara, Yoshihiro Ogawa
Journal: Endoscopy (2022)

Several traction techniques for endoscopic submucosal dissection (ESD) of gastric neoplasms have been reported to be useful [1] [2] [3] [4] [5]. We have previously reported an intralesional traction technique using a single traction band [5]. Since this creates a traction force within the lesion, theoretically, it could be applied to any gastric lesions. However, we do encounter cases in a few regions of the stomach where the traction force is insufficient. Here, we have proposed an intralesional cross-traction technique using dual traction bands ([Fig. 1]), which might overcome the weaknesses of the previous method ([Video 1]).